Model-Based Generation of Synthetic 3D Time-Lapse Sequences of
Multiple Mutually Interacting Motile Cells with Filopodia

D 2018

Model-Based Generation of Synthetic 3D Time-Lapse Sequences of Multiple Mutually Interacting Motile Cells with Filopodia

PETERLÍK, Igor, David SVOBODA, Vladimír ULMAN, Dmitry SOROKIN, Martin MAŠKA et. al.

Basic information

Original name

Model-Based Generation of Synthetic 3D Time-Lapse Sequences of Multiple Mutually Interacting Motile Cells with Filopodia

Authors

PETERLÍK, Igor (703 Slovakia, belonging to the institution), David SVOBODA (203 Czech Republic, belonging to the institution), Vladimír ULMAN (203 Czech Republic), Dmitry SOROKIN (643 Russian Federation) and Martin MAŠKA (203 Czech Republic, guarantor, belonging to the institution)

Edition

Cham, Simulation and Synthesis in Medical Imaging, p. 71-79, 9 pp. 2018

Publisher

Springer

Other information

Language

English

Type of outcome

Stať ve sborníku

Field of Study

10201 Computer sciences, information science, bioinformatics

Country of publisher

Germany

Confidentiality degree

není předmětem státního či obchodního tajemství

Publication form

electronic version available online

References:

URL

Impact factor

Impact factor: 0.402 in 2005

RIV identification code

RIV/00216224:14330/18:00101086

Organization unit

Faculty of Informatics

ISBN

978-3-030-00535-1

ISSN

DOI

http://dx.doi.org/10.1007/978-3-030-00536-8_8

UT WoS

000477752900008

Keywords in English

Simulation; 3D time-lapse sequence; Cell deformation; Cell interaction; Filopodia

Abstract

V originále

Complementing collections of 3D time-lapse image data with comprehensive manual annotations is an extremely laborious and often impracticable task, which hinders objective benchmarking of bioimage analysis workflows as well as training of widespread deep-learning-based approaches. In this paper, we present a novel simulation system capable of generating synthetic 3D time-lapse sequences of multiple mutually interacting cells with filopodial protrusions, accompanied by inherently generated reference annotations, in order to stimulate the development of fully 3D bioimage analysis workflows for filopodium segmentation and tracking in complex scenarios with multiple mutually interacting cells. The system integrates its predecessor, which was designed for single-cell, collision-unaware scenarios only, with proactive, mechanics-based handling of collisions between multiple filopodia, multiple cell bodies, or their combinations. We demonstrate its potential on two generated 3D time-lapse sequences of multiple lung cancer cells with curvilinear filopodia, which visually resemble confocal fluorescence microscopy image data.

Links

GJ16-03909Y, research and development project

Name: Vývoj spolehlivých metod pro automatizovanou kvantitativní charakterizaci buněčné motility ve fluorescenční mikroskopii

Investor: Czech Science Foundation

Citovat

PETERLÍK, Igor, David SVOBODA, Vladimír ULMAN, Dmitry SOROKIN and Martin MAŠKA. Model-Based Generation of Synthetic 3D Time-Lapse Sequences of Multiple Mutually Interacting Motile Cells with Filopodia. Online. In Simulation and Synthesis in Medical Imaging. Cham: Springer, 2018, p. 71-79. ISBN 978-3-030-00535-1. Available from: https://dx.doi.org/10.1007/978-3-030-00536-8_8.

@inproceedings{1424876,
   author = {Peterlík, Igor and Svoboda, David and Ulman, Vladimír and Sorokin, Dmitry and Maška, Martin},
   address = {Cham},
   booktitle = {Simulation and Synthesis in Medical Imaging},
   doi = {http://dx.doi.org/10.1007/978-3-030-00536-8_8},
   keywords = {Simulation; 3D time-lapse sequence; Cell deformation; Cell interaction; Filopodia},
   howpublished = {elektronická verze "online"},
   language = {eng},
   location = {Cham},
   isbn = {978-3-030-00535-1},
   pages = {71-79},
   publisher = {Springer},
   title = {Model-Based Generation of Synthetic 3D Time-Lapse Sequences of Multiple Mutually Interacting Motile Cells with Filopodia},
   url = {https://doi.org/10.1007/978-3-030-00536-8_8},
   year = {2018}
}

TY  - JOUR
ID  - 1424876
AU  - Peterlík, Igor - Svoboda, David - Ulman, Vladimír - Sorokin, Dmitry - Maška, Martin
PY  - 2018
TI  - Model-Based Generation of Synthetic 3D Time-Lapse Sequences of Multiple Mutually Interacting Motile Cells with Filopodia
PB  - Springer
CY  - Cham
SN  - 9783030005351
KW  - Simulation
KW  - 3D time-lapse sequence
KW  - Cell deformation
KW  - Cell interaction
KW  - Filopodia
UR  - https://doi.org/10.1007/978-3-030-00536-8_8
N2  - Complementing collections of 3D time-lapse image data with comprehensive manual annotations is an extremely laborious and often impracticable task, which hinders objective benchmarking of bioimage analysis workflows as well as training of widespread deep-learning-based approaches. In this paper, we present a novel simulation system capable of generating synthetic 3D time-lapse sequences of multiple mutually interacting cells with filopodial protrusions, accompanied by inherently generated reference annotations, in order to stimulate the development of fully 3D bioimage analysis workflows for filopodium segmentation and tracking in complex scenarios with multiple mutually interacting cells. The system integrates its predecessor, which was designed for single-cell, collision-unaware scenarios only, with proactive, mechanics-based handling of collisions between multiple filopodia, multiple cell bodies, or their combinations. We demonstrate its potential on two generated 3D time-lapse sequences of multiple lung cancer cells with curvilinear filopodia, which visually resemble confocal fluorescence microscopy image data.
ER  -

PETERLÍK, Igor, David SVOBODA, Vladimír ULMAN, Dmitry SOROKIN and Martin MAŠKA. Model-Based Generation of Synthetic 3D Time-Lapse Sequences of Multiple Mutually Interacting Motile Cells with Filopodia. Online. In \textit{Simulation and Synthesis in Medical Imaging}. Cham: Springer, 2018, p.~71-79. ISBN~978-3-030-00535-1. Available from: https://dx.doi.org/10.1007/978-3-030-00536-8\_{}8.

Detailed Information on Publication Record